Influence of housing system on antimicrobial resistance and population structure of extended-spectrum beta-lactamase–producing Escherichia coli in South Korean layer farms

Extended-spectrum β-lactamase (ESBL)–producing Escherichia coli are widespread in poultry production, posing serious public health risks. However, evidence from commercial layer farms—particularly environmental reservoirs—and direct comparisons between cage and floor housing systems remain limited. In this study, we aimed to investigate the prevalence, antimicrobial resistance (AMR) profiles, β-lactamase genotypes, and clonal diversity of ESBL-producing E. coli in floor- and cage-housed layer farms in South Korea to inform AMR risk assessment and control strategies. Eighty ESBL-producing E. coli isolates were recovered from 34 environmental samples collected across six farms (three floor-housed and three cage-housed layer farms). All isolates exhibited high resistance to ampicillin and third-generation cephalosporins, whereas susceptibility to imipenem and amikacin was retained. Resistance to tetracycline (45.2% vs. 15.8%; P = 0.005), chloramphenicol (64.3% vs. 31.6%; P = 0.005), and trimethoprim–sulfamethoxazole (54.8% vs. 18.4%; P = 0.001) was higher among floor-housed than cage-housed isolates, resulting in a higher prevalence of multidrug resistance in floor-housed isolates. Genotypic analysis identified bla CTX-M-14 (27.5%) and bla CTX-M-55 (21.3%) as the most prevalent ESBL genes. Among non-ESBL β-lactamase genes, bla TEM-30 and bla TEM-116 were more frequent in floor-housed isolates, whereas bla TEM-163 predominated in cage-housed isolates. Multilocus sequence typing showed reduced clonal diversity in floor-housed isolates, dominated by ST1718 and ST10, whereas cage-housed isolates displayed broader, more heterogeneous lineages. These findings indicate the association of layer housing systems with differences in AMR burden, β-lactamase allele distribution, and clonal structure of ESBL-producing E. coli , supporting housing-tailored biosecurity and farm-level surveillance to mitigate dissemination in layer production.